Note

Click here to download the full example code

Callosal bundles using AFQ API

An example using the AFQ API to find callosal bundles using the templates from: http://hdl.handle.net/1773/34926

import os.path as op

import plotly

from AFQ import api
from AFQ.definitions.mask import RoiMask
import AFQ.data as afd

Get some example data

Retrieves Stanford HARDI dataset.

afd.organize_stanford_data(clear_previous_afq=True)

Set tractography parameters (optional)

We make this tracking_params which we will pass to the AFQ object which specifies that we want 100,000 seeds randomly distributed in the ROIs of every bundle.

We only do this to make this example faster and consume less space.

tracking_params = dict(seed_mask=RoiMask(),
                       n_seeds=10000,
                       random_seeds=True,
                       rng_seed=42)

Initialize an AFQ object:

We specify bundle_info as the default bundles list (api.BUNDLES) plus the callosal bundle list. This tells the AFQ object to use bundles from both the standard and callosal templates.

myafq = api.AFQ(bids_path=op.join(afd.afq_home,
                                  'stanford_hardi'),
                dmriprep='vistasoft',
                bundle_info=api.BUNDLES + api.CALLOSUM_BUNDLES,
                tracking_params=tracking_params)

Visualizing bundles and tract profiles:

This would run the script and visualize the bundles using the plotly interactive visualization, which should automatically open in a new browser window.

bundle_html = myafq.viz_bundles(export=True, n_points=50)
plotly.io.show(bundle_html[0])

Out:

Optimizing level 2 [max iter: 10000]
Optimizing level 1 [max iter: 1000]
Optimizing level 0 [max iter: 100]
Optimizing level 2 [max iter: 10000]
Optimizing level 1 [max iter: 1000]
Optimizing level 0 [max iter: 100]
Optimizing level 2 [max iter: 10000]
Optimizing level 1 [max iter: 1000]
Optimizing level 0 [max iter: 100]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3358.13 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3320.91 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 15.01 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3081.78 MB/s]

  0%|          | 0/29 [00:00<?, ? MB/s]
 14%|#3        | 4/29 [00:00<00:00, 30.20 MB/s]
 52%|#####1    | 15/29 [00:00<00:00, 61.12 MB/s]
100%|##########| 29/29 [00:00<00:00, 108.41 MB/s]

  0%|          | 0/28 [00:00<?, ? MB/s]
 11%|#         | 3/28 [00:00<00:01, 22.55 MB/s]
 36%|###5      | 10/28 [00:00<00:00, 40.09 MB/s]
100%|##########| 28/28 [00:00<00:00, 83.58 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 2826.35 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3192.01 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 2912.71 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 2955.82 MB/s]

  0%|          | 0/23 [00:00<?, ? MB/s]
 17%|#7        | 4/23 [00:00<00:00, 30.09 MB/s]
 48%|####7     | 11/23 [00:00<00:00, 43.18 MB/s]
100%|##########| 23/23 [00:00<00:00, 68.87 MB/s]

  0%|          | 0/22 [00:00<?, ? MB/s]
 18%|#8        | 4/22 [00:00<00:00, 30.10 MB/s]
 45%|####5     | 10/22 [00:00<00:00, 38.86 MB/s]
100%|##########| 22/22 [00:00<00:00, 65.96 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 2365.65 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 2972.58 MB/s]

  0%|          | 0/2 [00:00<?, ? MB/s]
100%|##########| 2/2 [00:00<00:00, 30.15 MB/s]

  0%|          | 0/2 [00:00<?, ? MB/s]
100%|##########| 2/2 [00:00<00:00, 29.90 MB/s]

  0%|          | 0/24 [00:00<?, ? MB/s]
 17%|#6        | 4/24 [00:00<00:00, 30.13 MB/s]
 54%|#####4    | 13/24 [00:00<00:00, 52.02 MB/s]
100%|##########| 24/24 [00:00<00:00, 89.67 MB/s]

  0%|          | 0/24 [00:00<?, ? MB/s]
 17%|#6        | 4/24 [00:00<00:00, 30.04 MB/s]
 62%|######2   | 15/24 [00:00<00:00, 60.76 MB/s]
100%|##########| 24/24 [00:00<00:00, 88.83 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3374.34 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3204.20 MB/s]

  0%|          | 0/28 [00:00<?, ? MB/s]
 14%|#4        | 4/28 [00:00<00:00, 29.83 MB/s]
 43%|####2     | 12/28 [00:00<00:00, 47.18 MB/s]
100%|##########| 28/28 [00:00<00:00, 83.08 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3504.01 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3246.37 MB/s]

  0%|          | 0/25 [00:00<?, ? MB/s]
 16%|#6        | 4/25 [00:00<00:00, 29.17 MB/s]
 36%|###6      | 9/25 [00:00<00:00, 33.61 MB/s]
100%|##########| 25/25 [00:00<00:00, 73.23 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 15.00 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3527.59 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 2396.75 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 2720.04 MB/s]

  0%|          | 0/21 [00:00<?, ? MB/s]
 14%|#4        | 3/21 [00:00<00:00, 22.46 MB/s]
 52%|#####2    | 11/21 [00:00<00:00, 44.37 MB/s]
100%|##########| 21/21 [00:00<00:00, 78.09 MB/s]

  0%|          | 0/21 [00:00<?, ? MB/s]
 19%|#9        | 4/21 [00:00<00:00, 30.28 MB/s]
 52%|#####2    | 11/21 [00:00<00:00, 43.46 MB/s]
100%|##########| 21/21 [00:00<00:00, 78.81 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 2699.04 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3019.66 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 2908.67 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 2219.21 MB/s]

  0%|          | 0/29 [00:00<?, ? MB/s]
 14%|#3        | 4/29 [00:00<00:00, 30.34 MB/s]
 41%|####1     | 12/29 [00:00<00:00, 48.00 MB/s]
100%|##########| 29/29 [00:00<00:00, 87.55 MB/s]

  0%|          | 0/29 [00:00<?, ? MB/s]
 14%|#3        | 4/29 [00:00<00:00, 29.97 MB/s]
 34%|###4      | 10/29 [00:00<00:00, 38.69 MB/s]
100%|##########| 29/29 [00:00<00:00, 86.44 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 2935.13 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3123.09 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3724.96 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3858.61 MB/s]

  0%|          | 0/28 [00:00<?, ? MB/s]
 14%|#4        | 4/28 [00:00<00:00, 30.26 MB/s]
 39%|###9      | 11/28 [00:00<00:00, 43.38 MB/s]
100%|##########| 28/28 [00:00<00:00, 84.16 MB/s]

  0%|          | 0/27 [00:00<?, ? MB/s]
 15%|#4        | 4/27 [00:00<00:00, 30.05 MB/s]
 37%|###7      | 10/27 [00:00<00:00, 38.77 MB/s]
100%|##########| 27/27 [00:00<00:00, 80.49 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3748.26 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3474.98 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 2781.37 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3054.85 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 15.06 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3204.20 MB/s]

  0%|          | 0/32 [00:00<?, ? MB/s]
  9%|9         | 3/32 [00:00<00:01, 22.45 MB/s]
 34%|###4      | 11/32 [00:00<00:00, 44.32 MB/s]
100%|##########| 32/32 [00:00<00:00, 95.16 MB/s]

  0%|          | 0/30 [00:00<?, ? MB/s]
 13%|#3        | 4/30 [00:00<00:00, 29.88 MB/s]
 43%|####3     | 13/30 [00:00<00:00, 51.62 MB/s]
100%|##########| 30/30 [00:00<00:00, 89.12 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 2206.37 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 2511.56 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3371.63 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3289.65 MB/s]

  0%|          | 0/23 [00:00<?, ? MB/s]
 13%|#3        | 3/23 [00:00<00:00, 22.53 MB/s]
 52%|#####2    | 12/23 [00:00<00:00, 48.79 MB/s]
100%|##########| 23/23 [00:00<00:00, 85.55 MB/s]

  0%|          | 0/22 [00:00<?, ? MB/s]
 18%|#8        | 4/22 [00:00<00:00, 30.00 MB/s]
 50%|#####     | 11/22 [00:00<00:00, 43.02 MB/s]
100%|##########| 22/22 [00:00<00:00, 81.79 MB/s]

  0%|          | 0/26 [00:00<?, ? MB/s]
 15%|#5        | 4/26 [00:00<00:00, 30.13 MB/s]
 54%|#####3    | 14/26 [00:00<00:00, 56.35 MB/s]
100%|##########| 26/26 [00:00<00:00, 96.96 MB/s]

  0%|          | 0/23 [00:00<?, ? MB/s]
 17%|#7        | 4/23 [00:00<00:00, 30.07 MB/s]
 52%|#####2    | 12/23 [00:00<00:00, 47.67 MB/s]
100%|##########| 23/23 [00:00<00:00, 85.93 MB/s]

  0%|          | 0/2 [00:00<?, ? MB/s]
100%|##########| 2/2 [00:00<00:00, 33.71 MB/s]

  0%|          | 0/2 [00:00<?, ? MB/s]
100%|##########| 2/2 [00:00<00:00, 30.38 MB/s]

  0%|          | 0/2 [00:00<?, ? MB/s]
100%|##########| 2/2 [00:00<00:00, 30.06 MB/s]

  0%|          | 0/2 [00:00<?, ? MB/s]
100%|##########| 2/2 [00:00<00:00, 30.63 MB/s]

  0%|          | 0/2 [00:00<?, ? MB/s]
100%|##########| 2/2 [00:00<00:00, 30.18 MB/s]

  0%|          | 0/2 [00:00<?, ? MB/s]
100%|##########| 2/2 [00:00<00:00, 30.28 MB/s]

  0%|          | 0/2 [00:00<?, ? MB/s]
100%|##########| 2/2 [00:00<00:00, 30.21 MB/s]

  0%|          | 0/2 [00:00<?, ? MB/s]
100%|##########| 2/2 [00:00<00:00, 30.09 MB/s]

  0%|          | 0/2 [00:00<?, ? MB/s]
100%|##########| 2/2 [00:00<00:00, 30.61 MB/s]

  0%|          | 0/2 [00:00<?, ? MB/s]
100%|##########| 2/2 [00:00<00:00, 29.94 MB/s]

  0%|          | 0/2 [00:00<?, ? MB/s]
100%|##########| 2/2 [00:00<00:00, 1014.96 MB/s]

  0%|          | 0/2 [00:00<?, ? MB/s]
100%|##########| 2/2 [00:00<00:00, 30.13 MB/s]

  0%|          | 0/2 [00:00<?, ? MB/s]
100%|##########| 2/2 [00:00<00:00, 6898.53 MB/s]

  0%|          | 0/2 [00:00<?, ? MB/s]
100%|##########| 2/2 [00:00<00:00, 30.14 MB/s]

  0%|          | 0/2 [00:00<?, ? MB/s]
100%|##########| 2/2 [00:00<00:00, 3728.27 MB/s]

  0%|          | 0/2 [00:00<?, ? MB/s]
100%|##########| 2/2 [00:00<00:00, 30.16 MB/s]

  0%|          | 0/2 [00:00<?, ? MB/s]
100%|##########| 2/2 [00:00<00:00, 6340.60 MB/s]

  0%|          | 0/15 [00:00<?, ? MB/s]
 20%|##        | 3/15 [00:00<00:00, 24.58 MB/s]
 87%|########6 | 13/15 [00:00<00:00, 57.24 MB/s]
100%|##########| 15/15 [00:00<00:00, 60.34 MB/s]

  0%|          | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 4981.36 MB/s]

  0%|          | 0/1415 [00:00<?, ?it/s]
  0%|          | 1/1415 [00:00<02:45,  8.55it/s]
  0%|          | 2/1415 [00:00<09:06,  2.58it/s]
  0%|          | 4/1415 [00:06<42:42,  1.82s/it]
  1%|          | 14/1415 [00:06<07:55,  2.94it/s]
 73%|#######3  | 1040/1415 [00:06<00:01, 343.24it/s]
100%|##########| 1415/1415 [00:06<00:00, 227.06it/s]

  0%|          | 0/1156 [00:00<?, ?it/s]
 88%|########8 | 1020/1156 [00:00<00:00, 8467.94it/s]
100%|##########| 1156/1156 [00:00<00:00, 9571.27it/s]

  0%|          | 0/532 [00:00<?, ?it/s]
 95%|#########5| 508/532 [00:00<00:00, 4391.69it/s]
100%|##########| 532/532 [00:00<00:00, 4584.97it/s]

  0%|          | 0/304 [00:00<?, ?it/s]
100%|##########| 304/304 [00:00<00:00, 4292.21it/s]

  0%|          | 0/580 [00:00<?, ?it/s]
100%|##########| 580/580 [00:00<00:00, 7276.64it/s]

  0%|          | 0/546 [00:00<?, ?it/s]
 93%|#########3| 508/546 [00:00<00:00, 4968.64it/s]
100%|##########| 546/546 [00:00<00:00, 5323.08it/s]

  0%|          | 0/1377 [00:00<?, ?it/s]
 27%|##7       | 372/1377 [00:00<00:00, 3452.69it/s]
 73%|#######3  | 1012/1377 [00:00<00:00, 4025.73it/s]
100%|##########| 1377/1377 [00:00<00:00, 5369.65it/s]

  0%|          | 0/1232 [00:00<?, ?it/s]
 31%|###       | 380/1232 [00:00<00:00, 3357.65it/s]
 83%|########2 | 1020/1232 [00:00<00:00, 4382.70it/s]
100%|##########| 1232/1232 [00:00<00:00, 5110.93it/s]

  0%|          | 0/1190 [00:00<?, ?it/s]
 21%|##        | 248/1190 [00:00<00:00, 2096.78it/s]
 64%|######3   | 760/1190 [00:00<00:00, 3045.43it/s]
 89%|########8 | 1058/1190 [00:00<00:00, 2679.23it/s]
100%|##########| 1190/1190 [00:00<00:00, 3022.38it/s]

  0%|          | 0/998 [00:00<?, ?it/s]
 25%|##5       | 252/998 [00:00<00:00, 2061.32it/s]
 77%|#######6  | 764/998 [00:00<00:00, 3270.44it/s]
100%|##########| 998/998 [00:00<00:00, 4031.14it/s]

  0%|          | 0/1795 [00:00<?, ?it/s]
 28%|##8       | 508/1795 [00:00<00:00, 4699.62it/s]
 85%|########5 | 1532/1795 [00:00<00:00, 5769.98it/s]
100%|##########| 1795/1795 [00:00<00:00, 6601.09it/s]

  0%|          | 0/1665 [00:00<?, ?it/s]
 22%|##2       | 372/1665 [00:00<00:00, 3428.64it/s]
 61%|######    | 1012/1665 [00:00<00:00, 4595.86it/s]
100%|##########| 1665/1665 [00:00<00:00, 5678.39it/s]

  0%|          | 0/1376 [00:00<?, ?it/s]
 37%|###6      | 508/1376 [00:00<00:00, 4340.08it/s]
100%|##########| 1376/1376 [00:00<00:00, 7006.65it/s]

  0%|          | 0/1351 [00:00<?, ?it/s]
 38%|###7      | 508/1351 [00:00<00:00, 3986.31it/s]
100%|##########| 1351/1351 [00:00<00:00, 6683.13it/s]

  0%|          | 0/579 [00:00<?, ?it/s]
 66%|######5   | 380/579 [00:00<00:00, 3796.61it/s]
100%|##########| 579/579 [00:00<00:00, 4809.79it/s]

  0%|          | 0/702 [00:00<?, ?it/s]
100%|##########| 702/702 [00:00<00:00, 7813.94it/s]

  0%|          | 0/5570 [00:00<?, ?it/s]
 14%|#3        | 764/5570 [00:00<00:00, 5928.15it/s]
 28%|##7       | 1532/5570 [00:00<00:00, 6759.65it/s]
 40%|###9      | 2217/5570 [00:00<00:00, 6578.18it/s]
 55%|#####5    | 3068/5570 [00:00<00:00, 6971.41it/s]
 73%|#######3  | 4092/5570 [00:00<00:00, 5871.02it/s]
 92%|#########1| 5116/5570 [00:00<00:00, 5508.75it/s]
100%|##########| 5570/5570 [00:00<00:00, 6414.49it/s]

  0%|          | 0/5570 [00:00<?, ?it/s]
 18%|#8        | 1020/5570 [00:00<00:00, 8652.58it/s]
 55%|#####5    | 3068/5570 [00:00<00:00, 13345.83it/s]
100%|##########| 5570/5570 [00:00<00:00, 16609.78it/s]

  0%|          | 0/5570 [00:00<?, ?it/s]
 14%|#3        | 764/5570 [00:00<00:00, 6418.40it/s]
 37%|###6      | 2044/5570 [00:00<00:00, 6646.12it/s]
 63%|######3   | 3527/5570 [00:00<00:00, 9456.92it/s]
 82%|########1 | 4564/5570 [00:00<00:00, 7353.55it/s]
 97%|#########6| 5397/5570 [00:00<00:00, 6043.46it/s]
100%|##########| 5570/5570 [00:00<00:00, 6895.66it/s]

  0%|          | 0/5570 [00:00<?, ?it/s]
 18%|#8        | 1020/5570 [00:00<00:00, 8226.94it/s]
 55%|#####5    | 3068/5570 [00:00<00:00, 12047.25it/s]
 76%|#######6  | 4253/5570 [00:00<00:00, 11225.54it/s]
100%|##########| 5570/5570 [00:00<00:00, 14462.73it/s]

  0%|          | 0/5570 [00:00<?, ?it/s]
 14%|#3        | 764/5570 [00:00<00:00, 7075.04it/s]
 37%|###6      | 2044/5570 [00:00<00:00, 7534.83it/s]
 73%|#######3  | 4092/5570 [00:00<00:00, 7890.98it/s]
 92%|#########1| 5116/5570 [00:00<00:00, 7226.05it/s]
100%|##########| 5570/5570 [00:00<00:00, 8020.64it/s]

  0%|          | 0/5570 [00:00<?, ?it/s]
  7%|6         | 380/5570 [00:00<00:01, 3470.81it/s]
 18%|#8        | 1020/5570 [00:00<00:01, 3708.35it/s]
 37%|###6      | 2044/5570 [00:00<00:00, 3934.67it/s]
 46%|####5     | 2556/5570 [00:00<00:00, 3623.68it/s]
 55%|#####5    | 3068/5570 [00:00<00:00, 3460.14it/s]
 64%|######4   | 3580/5570 [00:01<00:00, 3234.40it/s]
 73%|#######3  | 4092/5570 [00:01<00:00, 3229.67it/s]
 83%|########2 | 4604/5570 [00:01<00:00, 3204.57it/s]
 92%|#########1| 5116/5570 [00:01<00:00, 3126.43it/s]
100%|##########| 5570/5570 [00:01<00:00, 3628.74it/s]

  0%|          | 0/5570 [00:00<?, ?it/s]
 14%|#3        | 764/5570 [00:00<00:00, 7273.05it/s]
 37%|###6      | 2044/5570 [00:00<00:00, 7669.24it/s]
 73%|#######3  | 4092/5570 [00:00<00:00, 8395.68it/s]
 92%|#########1| 5116/5570 [00:00<00:00, 7780.87it/s]
100%|##########| 5570/5570 [00:00<00:00, 8547.80it/s]

  0%|          | 0/5570 [00:00<?, ?it/s]
 14%|#3        | 764/5570 [00:00<00:00, 6704.93it/s]
 37%|###6      | 2044/5570 [00:00<00:00, 7426.43it/s]
 73%|#######3  | 4092/5570 [00:00<00:00, 8148.92it/s]
 92%|#########1| 5116/5570 [00:00<00:00, 7528.63it/s]
100%|##########| 5570/5570 [00:00<00:00, 8256.27it/s]

Total running time of the script: ( 20 minutes 29.110 seconds)

Gallery generated by Sphinx-Gallery

RecoBundles80 using AFQ API AFQ API